RetrogeneDB ID:

retro_eeur_238

Retrocopy
location
Organism:Hedgehog (Erinaceus europaeus)
Coordinates:scaffold_219319:3452..4139(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PRDX3
Ensembl ID:ENSEEUG00000009299
Aliases:None
Description:peroxiredoxin 3 [Source:HGNC Symbol;Acc:9354]


Retrocopy-Parental alignment summary:






>retro_eeur_238
ACTTCCACCTCAGCAGCCCTAAGACCTACTGTATCCCGATGGACAAATGGATTGTGGGCAGCTTCCAGGTAGGCCGGACT
CGCCTTTAGCACCAGTTCCTCGCTCCAGGCACCCGTCATCGCAGAGCTGCGCTCCATTTCAAGGGCACAGCTGTTGTCAA
TAGGGAGTTCAAGGAACTGAGCCTTGATGACTTCAAGGGGAAGCACTTGGCGATTTTCTTCTACCCTTTGGATTTTACCT
TCATATCTCCTACAAAGATCGTCGCTTTCAGTGACAAAGCCAATGAGTTTCATGATGTGAACTGTGAGGTCGTCGCCGTG
TCTGTGGATTCCCACTTCTGCCACCTCGCCTGGATAAACACGCCGAGGAAGGACAGTGGTCTGGGCCACATGAACATCCC
GCTCCTGTAAGATTTGATGAAATAGATCTCCCGGGACTACGGTGTGCTTGCTACTTGAGGTCTCACCCTGAGAGGCCTCT
TCATAATCGACTCCAATGGAGTCCACAAGCATATGAAGTGTCAGTGACCTGGCGGTGGGCCACAGTGTGAAGGAGACTCT
CTGCCTGGTCGAGGCCTTCCAGTTGGTGGAAGCCCATGGAGAGGTCTGACCGGCCAACTGGAAGCCAGATTCTCCCACAA
TCAAGCCGCATCCAATGGCTTCCAAAAAATACTTCAAGAAAGTGAAT

ORF - retro_eeur_238 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.88 %
Parental protein coverage: 90.55 %
Number of stop codons detected: 5
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalTSASAALRPAASRLTNGLWAASTQARLAFSTSSSLQTPAVTE-HAPHFKGTAVVNGEFKELSLDDFKGKY
TS.SAALRP..SR.TNGLWAAS..A.LAFSTSSSLQ.P...E..A.HFKGTAVVN.EFKELSLDDFKGK.
RetrocopyTSTSAALRPTVSRWTNGLWAASR*AGLAFSTSSSLQAPVIAE<AALHFKGTAVVNREFKELSLDDFKGKH
ParentalLVLFFYPLDFTFVCPTEIIAFSDKANEFHDVNCEVIAASVDSHFCHLAWINTPRKNGGLGHMNIPLLSDL
L..FFYPLDFTF..PT.I.AFSDKANEFHDVNCEV.A.SVDSHFCHLAWINTPRK..GLGHMNIPLL.DL
RetrocopyLAIFFYPLDFTFISPTKIVAFSDKANEFHDVNCEVVAVSVDSHFCHLAWINTPRKDSGLGHMNIPLL*DL
ParentalTKQISRDYGVLLEGSGLALRGLFIIDPNGVIKHM-SVNDLPVGRSVEETLRLVKAFQFVEAHGEVCPANW
.K.ISRDYGVL....GL.LRGLFIID.NGV.KHM.SV.DL.VG.SV.ETL.LV.AFQ.VEAHGEV.PANW
RetrocopyMK*ISRDYGVLAT-*GLTLRGLFIIDSNGVHKHM>SVSDLAVGHSVKETLCLVEAFQLVEAHGEV*PANW
ParentalTPDSPTIKPHPTASKEYFEKVN
.PDSPTIKPHP.ASK.YF.KVN
RetrocopyKPDSPTIKPHPMASKKYFKKVN

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP017611_brain 0 .00 RPM 24 .82 RPM
SRP017611_kidney 0 .00 RPM 89 .08 RPM
SRP017611_liver 0 .00 RPM 63 .35 RPM

ChIP-Seq - click to see more details

Erinaceus europaeus was not studied using ChIP-Seq data.

EST - click to see more details

Erinaceus europaeus was not studied using EST data.

TSS - click to see more details

Erinaceus europaeus was not studied using FANTOM5 data.

Lab - click to see more details

retro_eeur_238 was not experimentally validated.

Retrocopy orthology:
Erinaceus europaeus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.
Parental genes homology:
Parental genes homology involve 23 parental genes, and 45 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000087311 retrocopy
retro_btau_562,
Canis familiaris ENSCAFG000000121093 retrocopies
retro_cfam_1322, retro_cfam_219, retro_cfam_9,
Callithrix jacchus ENSCJAG000000196363 retrocopies
retro_cjac_1333, retro_cjac_3082, retro_cjac_653,
Ciona savignyi ENSCSAVG000000012091 retrocopy
retro_csav_6,
Dasypus novemcinctus ENSDNOG000000013593 retrocopies
retro_dnov_1052, retro_dnov_2373, retro_dnov_745,
Equus caballus ENSECAG000000170261 retrocopy
retro_ecab_408,
Erinaceus europaeus ENSEEUG00000009299 1 retrocopy
retro_eeur_238 ,
Homo sapiens ENSG000001656723 retrocopies
retro_hsap_1253, retro_hsap_2587, retro_hsap_2653,
Gorilla gorilla ENSGGOG000000263641 retrocopy
retro_ggor_986,
Macropus eugenii ENSMEUG000000077323 retrocopies
retro_meug_1219, retro_meug_1735, retro_meug_62,
Microcebus murinus ENSMICG000000076271 retrocopy
retro_mmur_475,
Myotis lucifugus ENSMLUG000000128713 retrocopies
retro_mluc_1203, retro_mluc_1522, retro_mluc_2069,
Macaca mulatta ENSMMUG000000082942 retrocopies
retro_mmul_1307, retro_mmul_1517,
Monodelphis domestica ENSMODG000000092861 retrocopy
retro_mdom_1062,
Mustela putorius furoENSMPUG000000030741 retrocopy
retro_mputfur_1032,
Mus musculus ENSMUSG000000249971 retrocopy
retro_mmus_2443,
Nomascus leucogenys ENSNLEG000000166983 retrocopies
retro_nleu_1521, retro_nleu_2118, retro_nleu_2453,
Oryctolagus cuniculus ENSOCUG000000173342 retrocopies
retro_ocun_135, retro_ocun_1434,
Pongo abelii ENSPPYG000000027001 retrocopy
retro_pabe_1906,
Pan troglodytes ENSPTRG000000029921 retrocopy
retro_ptro_29,
Ictidomys tridecemlineatus ENSSTOG000000025372 retrocopies
retro_itri_1098, retro_itri_1753,
Tupaia belangeri ENSTBEG000000110645 retrocopies
retro_tbel_3138, retro_tbel_3994, retro_tbel_710, retro_tbel_770, retro_tbel_811,
Tursiops truncatus ENSTTRG000000108782 retrocopies
retro_ttru_1703, retro_ttru_881,


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